The present-day concept of toxins in pathogenesis has acquired an important place in the arena of plant pathology. Because once the toxic metabolite of the pathogen is identified and characterized, it opens up many ways for combating the pathogen. Microbes use toxins as a weapon to cause damage and eventually destroy host cells. Plant pathogenic bacteria and fungi damage their host by producing diffusible toxins. These toxins induce several symptoms such as chlorosis, necrosis, water soaking, and wilting, which lead to the death of the plants. These toxins (secondary metabolites) are dangerous to the plants even in minute concentrations, and many of the toxins reproduce at least a few symptoms of relevant fungal or bacterial diseases. Plant pathogens use toxins as weapons to infect susceptible hosts. There has been significant progress in understanding these microbial toxins’ nature, structure, and their mode of action, which is discussed in this article. In addition to being employed to determine plant disease resistance, screening for disease-resistant mutants, and managing disease, studying pathogenic toxins and their underlying mechanisms for pathogenicity is crucial to understand the host-pathogen interactions.